SUMMARY: Whole-genome sequencing has revolutionized the study of genetics. Genotyping-by-sequencing is now a viable method of genotyping, yet the bioinformatics involved can be daunting if not prohibitive for some laboratories. Here we present ArrayMaker, a user-friendly tool that extracts accurate single nucleotide polymorphism genotypes at pre-defined loci from whole-genome alignments and presents them in a standard genotyping format compatible with association analysis software and datasets genotyped on commercial array platforms. Using this tool, geneticists with only basic computing ability can genotype samples at any desired list of markers, facilitating genome-wide association analysis, fine mapping, candidate variant assessment, data sharing and compatibility of data sourced from multiple technologies. AVAILABILITY AND IMPLEMENTATION: ArrayMaker is licensed under The MIT License and can be freely obtained at https://github.com/cw2014/ArrayMaker/. The program is implemented in Perl and runs on Linux operating systems. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: [email protected].